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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

Title: Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.))

Author
item Yan, Wengui
item Li, Yong
item Agrama, Hesham
item Luo, Dagang
item Gao, Fangyuan
item Ren, Guangjun

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2009
Publication Date: 10/1/2009
Citation: Yan, W., Li, Y., Agrama, H.A., Luo, D., Gao, F., Ren, G. 2009. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Molecular Breeding. 24(3):277-292.

Interpretive Summary: Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core sample from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. A mixed linear model combining PC-matrix and K-matrix was adapted for marker-trait association mapping. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played a major role and explained 35% of phenotypic variation for DStgE and 17% for SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 was associated with all three correlated spikelet traits. These correspondences between trait-trait correlation and trait-marker association provide further confirmation to the mapped associations.

Technical Abstract: Hybrid rice exhibits a yield advantage of 15 to 20 percent (or more than one ton of paddy rice per hectare) over the best traditional varieties. Because rice plants are self-pollinating, commercial production of hybrid seed plays a key role in successful implementation of hybrid rice. Stigma exsertion and associated spikelet traits are important to increase pollination opportunity for a higher yield of hybrid seed because the exserted stigmas remain viable up to six days. A mini-core sample from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. As a result, we identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played a major role and explained 35% of the phenotypic variation for DStgE and 17% for SStgE. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 was associated with all three correlated spikelet traits. These correspondences between trait-trait correlation and trait-marker association confirmed the associations. These identified associations could be used in marker-assisted breeding to improve stigma exsertion in rice.

Last Modified: 8/24/2016
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